Mass spectrometry, combinatorial library

The new field of molecular diversity raises three issues which need to be addressed by the organic analytical chemistry community (i) What tools can we use for following solid-phase reactions (ii) How can we analyze all these samples (iii) How much characterization of libraries is possible or appropriate This chapter deals with these problems and reviews the literature since a similar review written in June 1995 [2] (earlier seminal publications are described where appropriate). Other analytical issues such as decoding of combinatorial libraries or the applications of affinity separations and single-bead mass spectrometry for library deconvolution are dealt with in other chapters of this book. 

Mass spectrometry is an indispensable analytical tool in chemistry, biochemistry, pharmacy, and medicine. No student, researcher or practitioner in these disciplines can really get along without a substantial knowledge of mass spectrometry. Mass spectrometry is employed to analyze combinatorial libraries [1,2] sequence biomolecules, [3] and help explore single cells [4,5] or other planets. [6] Structure elucidation of unknowns, environmental and forensic analytics, quality control of drugs, flavors and polymers they all rely to a great extent on mass spectrometry. [7-11]... 

Enjalbal, C. Maux, D. Combarieu, R. Martinez, J. Aubagnac, J.-L. Imaging Combinatorial Libraries by Mass Spectrometry From Peptide to Organic-Supported Syntheses. J. Comb. Chem. 2003, 5, 102-109. 

Kaur, S., McGuire, L., Tang, D., Dollinger, G., Heubner, V. Affinity selection and mass spectrometry-based strategies to identify lead compounds in combinatorial libraries. J. Prot. Chem. 1997, 16, 505-511. 

Zhao, Y.-Z., van Breemen, R.B., Nikolic, D., Huang, C.-R., Woodbury, C.P., Schilling, A., Venton, D.L. Screening solution-phase combinatorial libraries using pulsed ultrafiltration/electrospray mass spectrometry. J. Med. Chem. 1997, 40, 4006-4012. 

Kirby, D.P., Vouros, P., Karger, B.L. Affinity capillary electrophoresis-mass spectrometry for screening combinatorial libraries. J. Am. 

E. A. An affinity selection-mass spectrometry method for the identification of small molecule ligands from self-encoded combinatorial libraries, discovery of a novel antagonist of E. coli dihydrofolate reductase. Int. J. Mass. Spectrom. 2004, 238, 77-83. 

Hughes, L Design of self-coded combinatorial libraries to facilitate direct analysis of ligands by mass spectrometry. J. Med. Chem. 1998, 41, 3804-3811. 

Shin YG, van Breemen RB Analysis and screening of combinatorial libraries using mass spectrometry. Biopharm Drug Dispos 2001, 22, 353-372. 

Schilling A, Venton DL Screening solution-phase combinatorial libraries using pulsed ultrafiltration/ electrospray mass spectrometry. J Med Chem 1997, 40, 4006-4012. 

For those readers who are not yet familiar with mass spectrometry, the introduction provides an explanation of the basics of mass spectrometry and its instrumentation as well as practical aspects and applications in bioanalysis. Next, a block of three chapters shows different affinity selection procedures suitable to identify hits from combinatorial compound libraries. This subject, being metaphorically speaking a search for a needle in a haystack, is of outstanding relevance for big pharma . The techniques described here offer real high throughput capabilities and are implemented already in the routine industrial screening... 

Roulsen, S.-A. Direct screening of a dynamic combinatorial library using mass spectrometry. J. Am. Soc. Mass Spectrom. 2006,17, 1074-1080. 

YH Chu, YM Dunayevskiy, DB Kirby, P Vouros, BL Karger. Affinity capillary electrophoresis—mass spectrometry for screening combinatorial libraries. J Am Chem Soc 118 7827-7835, 1996. 

YH Chu, DP Kirby, BL Karger. Free-solution identification of candidate peptides from combinatorial libraries by affinity capillary electrophoresis/mass spectrometry. J Am Chem Soc 117 5419-5420, 1995. 

ESI-MS has been used for the quantification of a number of substrates and products of enzymatic reactions [56,57]. Hsieh et al. report the use of ion spray mass spectrometry (a technical variation of electrospray ionization) coupled to HPLC for the kinetic analysis of enzymatic reactions in real time [58]. The hydrolysis of dinucleotides with bovine pancreatic ribonuclease A and the hydrolysis of lactose with 3-galactosidase were monitored and the resulting data were used for the estimation of and v x of these reactions. Another field of application of electrospray mass spectrometry is the screening of combinatorial libraries for potent inhibitors [31,59]. 

Combinatorial methods were also applied in the discovery of new catalysts for the low-temperature oxidation213 and oxidative dehydrogenation of propane.214 A 144-member catalyst library was screened by photothermal deflection spectroscopy and mass spectrometry to find the most active compositions of V-Al-Nb and Cr-Al-Nb oxides for the oxidative dehydrogenation of ethane.215 The ternary combination V(45)-Sn(45)-Mo(10)-O selected by laser-induced fluorescence imaging gave much higher yield than did V205 in the selective oxidation of naphthalene to naphthoquinone.216... 

Another use for combinatorial libraries has been the screening of peptides for antimicrobrial properties. In this case, the design of the library is based on antimicrobial peptides found in nature. A combinatorial synthesis is used to find alternative unnatural amino acids expected to mimic the antimicrobial properties.23 Peptide libraries also have been used to find compounds that could bind the lytic peptide mellitin.24 The library was synthesized in solution phase, purified, and evaluated using time-of-flight mass spectrometry (TOF-MS). The sequences determined to bind to mellitin contained hydrophobic pairs. By binding to mellitin, they were able to prevent the cell-surface mellitin interaction. This is an example of a peptide library able to afford compounds that interact with other small peptides without having to find an interacting protein first. 

Nawrocki, J. P., Wigger, M., Watson, C. H., Hayes, T. W., Senko, M. W., Benner, S. A., and Eyler, J. R. (1996). Analysis of combinatorial libraries using electrospray Fourier transform ion cyclotron resonance mass spectrometry. Rapid Commun. Mass Spectrom. 10 1860-1864. 

Annis D.A., Athanasopoulos J., Curran P.J., Felsch J.S., Kalghatgi K., Lee W.H., Nash H.M., Orminati J.P.A., Rosner K.E., Shipps GW., Thaddupathy G.R.A., Tyler A.N., Vilenchik L., Wagner C.R., Wintner E.A., An affinity selection-mass spectrometry method for the identification of small molecule ligands from self-encoded combinatorial libraries. Discovery of a novel antagonist of E. coli dihydrofolate reductase Int. J. Mass Spectrom. 2004, 238, 77-83. 

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